Limnology and Oceanography | 2021
Evaluating the congruence between DNA ‐based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36‐month time series from a temperate monomictic lake
Abstract
Paleolimnological studies are central for identifying long-term changes, yet many studies rely on bioindicators that deposit detectable subfossils in sediments, such as diatoms and cladocerans. Emerging DNA-based approaches are expanding the taxonomic diversity that can be investigated. However, as sedimentary DNA-based approaches are expanding rapidly, calibration work is required to determine the advantages and limitations of these techniques. In this study, we assessed the congruence between morphological and DNA-based approaches applied to sediment trap samples for diatoms and crustaceans using both intracellular and extracellular DNA. We also evaluated which taxa are deposited in sediment traps from the water column to identify potential paleolimnological bioindicators of environmental variations. Based on 18S rRNA gene amplicons, we developed and analyzed a micro-eukaryotic, monthly time series that spanned 3 years and was comprised of paired water column and sediment trap samples from Cultus Lake, British Columbia, Canada. Comparisons of assemblages derived from our genetic and morphological analyses using RV coefficients revealed significant correlations for diatoms, but weaker correlations for crustaceans. Intracellular DNA reads correlated more strongly with diatom morphology, while extracellular DNA reads correlated more strongly with crustacean morphology. Additional analyses of amplicon sequence variants shared between water and sediment trap samples revealed a wide diversity of taxa to study in paleolimnology, including Ciliophora, Dinoflagellata, Chytridiomycota, Chrysophyceae, and Cryptophyceae. Partial RDAs identified significant environmental predictors of these shared assemblages. Overall, our study demonstrates the effectiveness of DNA-based approaches to track community dynamics from sediment samples, an essential step for successful paleolimnological studies. Over the past century, anthropogenic activities and climate change have induced significant alterations to freshwater ecosystems, with an intensification of stressors since the 1970s (Reid et al. 2018). Paleolimnological records have played a central role in quantifying the rate and magnitude of past ecological dynamics and have served to identify the major drivers of ecosystem change (Smol 2008; Bennion et al. 2011). Paleolimnological time series have been useful in evaluating the adequacy of management practices (Perga et al. 2010) and may inform future scenario development (Smol 2008; Gillson and Marchant 2014; SaulnierTalbot 2016). Biological community changes in the sediment record have relied mostly on the study of a small subset of aquatic taxa that deposit detectable subfossils including diatom valves (Battarbee et al. 2001), chrysophyte cysts and scales (Zeeb and Smol 2001) and cladoceran (Alric and Perga 2011) and chironomid remains (Walker 2001). However, many pelagic organisms do not preserve as visually identifiable subfossils in the sediments (e.g., fungi, soft algae, rotifers, and copepods), yet may be useful as bioindicators of environmental change. Applying DNA-based approaches to lake sediments has the potential to expand the taxonomic diversity that can be *Correspondence: [email protected] This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. Additional Supporting Information may be found in the online version of this article.